PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation

PICKLE (PKL) encodes a chromodomain helicase DNA-binding 3-type chromatin remodeling factor in Arabidopsis. Although PKL is known to influence plant development and environmental responses, its role in regulating chromatin states remains unclear. Using ChIP-seq with an endogenous PKL antibody, we identified 3534 high-confidence PKL-binding sites across the genome. PKL occupancy significantly overlapped with TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs), PHYTOCHOME INTERACTING FACTORs (PIFs), and ELONGATED HYPOCOTYL 5 (HY5) near the target gene transcription start site, and binding at shared targets decreased in the corresponding mutants, indicating that these transcription factors facilitate PKL recruitment. PKL-bound loci were enriched for H3K4me2 and H3K4me3, and loss of PKL reduced H3K4me2 levels. PKL also interacts with WDR5A and facilitates its chromatin occupancy at shared loci, which may contribute to H3K4 methylation regulation. Moreover, PKL-associated regions displayed spatial clustering coordinated with PKL and its transcription factor partners, reflecting chromatin organization at specific genes, a feature conserved for PKL and TCP homologs in Marchantia. Overall, our findings reveal that PKL promotes H3K4me2 levels, establishes a permissive chromatin environment, and orchestrates the spatial clustering of its genomic targets.